Sun Oct 9 22:34:28 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 22:34:28 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: LYS 506 has a net charge of 1.5000 !!! WARNING: SEP 654 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6335196 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -45.81700 2.833000 ymin,ymax (A): -44.36800 8.177000 zmin,zma (A): -10.12500 46.06900 x,y,z range (A): 48.65000 52.54500 56.19400 scale (grids/A): 0.6335196 object centre (A): -21.49200 -18.09550 17.97200 number of atom coordinates read : 2493 total number of charged atoms : 2444 net assigned charge : 6.025012 assigned positive charge : 392.3799 centred at (gu) : 88.76685 89.79034 90.76370 assigned negative charge : -386.3557 centred at (gu) : 88.83706 89.80968 90.82038 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6793 nv = 96 ne = 84 npr = 47440 no. pairs analyzed = 47440 no. exposed pairs = 3236 no. arc points = 23073 no. surface atoms = 1099 nbur = 1394 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 308 mr = 3502 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.1800000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2403 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0770728E-08 1.9047679E-09 midg,1,midg; midg,igrid,midg 9.4895602E-09 5.1024638E-09 1,midg,midg; igrid,midg,midg 1.8218701E-08 3.4387845E-10 gauss-seidel spectral radius is 0.9870896 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 22:34:29 rms-change max change #iterations 0.1374094 20.01375 at 10iterations 1.3161387E-02 2.104480 at 20iterations 1.2730433E-03 0.2052078 at 30iterations 1.2335162E-04 1.8009186E-02 at 40iterations 1.1940141E-05 1.8565655E-03 at 50iterations finished qdiffx linear iterations at : 22:34:32 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.1940141E-05 1.8565655E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 22:34:32 3.411u 0.173s 0:03.95 90.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 22:34:32 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: LYS 506 has a net charge of 1.5000 !!! WARNING: SEP 654 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.900559 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -45.81700 2.833000 ymin,ymax (A): -44.36800 8.177000 zmin,zma (A): -10.12500 46.06900 x,y,z range (A): 48.65000 52.54500 56.19400 scale (grids/A): 1.900559 object centre (A): -21.49200 -18.09550 17.97200 number of atom coordinates read : 2493 total number of charged atoms : 2444 net assigned charge : 6.025012 assigned positive charge : 392.3799 centred at (gu) : 86.29970 89.37062 92.29040 assigned negative charge : -386.3557 centred at (gu) : 86.51081 89.42888 92.46064 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23073 grid for indexing accessible points = 1.400000 m= 24588 mr = 48938 m= 3806 mr = 17613 m= 219 mr = 2287 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 743 time to turn everything in is 0.3700000 number of dielectric boundary points 32675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19240 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6335196 object centre at (A) : -21.49200 -18.09550 17.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1439685E-03 2.6975611E-02 midg,1,midg; midg,igrid,midg 6.4922301E-03 1.8108085E-02 1,midg,midg; igrid,midg,midg 1.5677599E-02 -9.1084577E-03 gauss-seidel spectral radius is 0.9986237 estimated iterations to convergence 214 setup time was (sec) 0.5900000 now iterating at: 22:34:33 rms-change max change #iterations 4.200118 180.1356 at 10iterations 1.947813 64.41875 at 20iterations 0.9106332 31.00867 at 30iterations 0.4242475 14.69481 at 40iterations 0.1971042 6.315271 at 50iterations 9.2129722E-02 2.993185 at 60iterations 4.2824090E-02 1.327975 at 70iterations 2.0041781E-02 0.6875744 at 80iterations 9.3346238E-03 0.2841644 at 90iterations 4.3641403E-03 0.1475201 at 100iterations 2.0249391E-03 6.4965248E-02 at 110iterations 9.4322662E-04 2.9342651E-02 at 120iterations finished qdiffx linear iterations at : 22:34:40 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 9.4322662E-04 2.9342651E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 22:34:41 7.905u 0.180s 0:08.34 96.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 22:34:41 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: LYS 506 has a net charge of 1.5000 !!! WARNING: SEP 654 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.850838 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -45.81700 2.833000 ymin,ymax (A): -44.36800 8.177000 zmin,zma (A): -10.12500 46.06900 x,y,z range (A): 48.65000 52.54500 56.19400 scale (grids/A): 2.850838 object centre (A): -21.49200 -18.09550 17.97200 number of atom coordinates read : 2493 total number of charged atoms : 2444 net assigned charge : 6.025012 assigned positive charge : 392.3799 centred at (gu) : 84.44951 89.05582 93.43561 assigned negative charge : -386.3557 centred at (gu) : 84.76625 89.14324 93.69109 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 168999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23073 grid for indexing accessible points = 1.400000 m= 81092 mr = 119334 m= 27611 mr = 65120 m= 6719 mr = 21619 m= 1014 mr = 4895 m= 68 mr = 702 m= 0 mr = 34 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2454 time to turn everything in is 0.9100000 number of dielectric boundary points 73799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19547 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.900559 object centre at (A) : -21.49200 -18.09550 17.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8868827E-02 0.2281660 midg,1,midg; midg,igrid,midg -0.1135916 0.2824876 1,midg,midg; igrid,midg,midg 0.1949366 -0.1786596 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 1.150000 now iterating at: 22:34:42 rms-change max change #iterations 9.868774 370.9040 at 10iterations 5.758268 153.1672 at 20iterations 3.342662 67.95171 at 30iterations 1.930365 37.58604 at 40iterations 1.118338 22.06981 at 50iterations 0.6423460 12.57029 at 60iterations 0.3696672 7.043365 at 70iterations 0.2131888 3.820752 at 80iterations 0.1224959 2.304000 at 90iterations 7.0249893E-02 1.384323 at 100iterations 4.0414341E-02 0.7556515 at 110iterations 2.3231009E-02 0.4445243 at 120iterations 1.3338712E-02 0.2480574 at 130iterations 7.6579126E-03 0.1439781 at 140iterations 4.3996437E-03 8.2176208E-02 at 150iterations 2.5219221E-03 4.4933796E-02 at 160iterations 1.4497867E-03 2.8944612E-02 at 170iterations 8.3319168E-04 1.6393185E-02 at 180iterations finished qdiffx linear iterations at : 22:34:53 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 8.3319168E-04 1.6393185E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 22:34:54 12.795u 0.212s 0:13.29 97.8% 0+0k 0+0io 0pf+0w